The vision is a very old scanner. Does it actually output DICOM? 15 years ago it only output IMA files. If so, then try mri_convert -it siemens file.ima file.mgh
On 11/05/2013 06:54 AM, Philipp Heimbeck wrote:
Hello!
I'm encountering a problem with converting fMRI-Data from dicom- to NIfTI-files (single file). The problem only occurs with data aquired on Siemens Vision, data from Siemens Trio work just fine. The "Siemens ASCII header" is missing (files have not been anonymized) and every dicom-file has its own series number. This is true for all functional data (10 subjects, one run each). Other programs can't convert these dicom-files either (dcm2nii, NIfTI-1 converter for BVQX). Do you know if there is a possible solution for this problem?
In more detail, when running mri_convert, the following happens:
... Getting Series No Scanning Directory INFO: Found 218 files in ../run INFO: Scanning for Series Number 67 INFO: found 1 files in series INFO: loading series header info.
INFO: sorting. RunNo = 66
WARNING: file ../MR.9500.260 does not contain a Siemens ASCII header has this file been anonymized? Proceeding as best as I can ...
INFO: (512 512 1), nframes = 1, ismosaic=0 PE Dir COL COL FileName ../MR.9500.260 Identification NumarisVer VB33D ScannerModel MAGNETOM VISION PatientName deleted, shows correctly Date and time StudyDate deleted, shows correctly StudyTime 150948.046000 SeriesTime 153015.877000 AcqTime 153606.293000 Acquisition parameters PulseSeq ep_fid Protocol unknown PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 60 InversionTime -1 RepetitionTime 60 PhEncFOV 0 ReadoutFOV 0 Image information RunNo 66 SeriesNo 67 ImageNo 260 NImageRows 512 NImageCols 512 NFrames 1 SliceArraylSize 0 IsMosaic 0 ImgPos 96.0000 80.1658 98.1990 VolRes 0.3750 0.3750 3.0000 VolDim 512 512 1 Vc -1.0000 0.0000 -0.0000 Vr -0.0000 -0.9848 -0.1736 Vs -nan -nan -nan VolCenter -nan -nan -nan TransferSyntaxUID unknown INFO: no Siemens slice order reversal detected (good!). TR=60.00, TE=60.00, TI=-1.00, flip angle=90.00 i_ras = (-1, 0, -0) j_ras = (-0, -0.984808, -0.173648) k_ras = (-nan, -nan, -nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is -nan, matrix is: -0.375 -0.000 -nan -nan; 0.000 -0.369 -nan -nan; -0.000 -0.065 -nan -nan; 0.000 0.000 0.000 1.000;
If there's any help, I'm glad to hear it. And if the answer is "no, the data is gone forever", this would be a helpful response, too.
Philipp
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